N - mixture models by species
modelling N by site to get relative abundance
abundance by site will be used as a cov on predator occupancy
7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ
Species: Â Â Â Â Chipmunk
Detections by Year:
|
Yr
|
2016
|
2017
|
2018
|
2019
|
2020
|
|
sites
|
19
|
31
|
19
|
32
|
26
|
|
detections
|
15
|
31
|
14
|
26
|
43
|
|
N.dot.model
|
10
|
16
|
7
|
8
|
22
|
WAIC
Models by WAIC:
|
model
|
description
|
WAIC
|
N.total.est
|
|
fm7
|
counts
|
4.060804
|
127
|
|
fm5
|
jdt + jdtSq
|
830.680975
|
59
|
|
fm6
|
lure + jdt + jdtSq
|
831.757572
|
62
|
|
fm2
|
jdt
|
857.470979
|
61
|
|
fm4
|
lure + jdt
|
858.315210
|
67
|
|
fm3
|
lure
|
859.204048
|
60
|
|
fm1
|
dot
|
865.500876
|
63
|
Model summaries:
model: fm1
summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
p[1]
|
NA
|
1486
|
0.052
|
0.046
|
0.01
|
0.09
|
0
|
0.9977
|
|
p[2]
|
NA
|
4787
|
0.076
|
0.07
|
0.04
|
0.11
|
0
|
1.001
|
|
p[3]
|
NA
|
4902
|
0.053
|
0.047
|
0.02
|
0.08
|
0
|
1.001
|
|
p[4]
|
NA
|
7512
|
0.124
|
0.119
|
0.07
|
0.17
|
0
|
1.001
|
|
p[5]
|
NA
|
4250
|
0.064
|
0.062
|
0.04
|
0.09
|
0
|
1.001
|
|
lambda[1]
|
NA
|
162
|
1.122
|
0.566
|
0.22
|
1.65
|
0
|
1.0013
|
|
lambda[2]
|
NA
|
5123
|
0.752
|
0.637
|
0.37
|
1.11
|
0
|
1.001
|
|
lambda[3]
|
NA
|
3172
|
0.496
|
0.342
|
0.13
|
0.81
|
0
|
1.0009
|
|
lambda[4]
|
NA
|
9210
|
0.271
|
0.22
|
0.10
|
0.42
|
0
|
1.001
|
|
lambda[5]
|
NA
|
4293
|
0.991
|
0.867
|
0.51
|
1.44
|
0
|
1.001
|
|
N[66]
|
NA
|
5684
|
1.201
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[100]
|
NA
|
10000
|
0.002
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[81]
|
NA
|
9382
|
1.024
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[68]
|
NA
|
4898
|
1.478
|
1
|
1.00
|
2.00
|
0
|
1.0001
|
|
N[33]
|
NA
|
7970
|
1.143
|
err
|
1.00
|
2.00
|
err
|
err
|
p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[66]

N[100]

N[81]

N[68]

N[33]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
jdt
|
9017
|
0.206
|
0.198
|
0.05
|
0.38
|
0.13548
|
0.9789
|
|
alpha0
|
NA
|
4853
|
-2.666
|
-2.654
|
-2.91
|
-2.42
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9430
|
0.572
|
0.485
|
0.24
|
0.87
|
0
|
1.001
|
|
lambda[2]
|
NA
|
8256
|
0.777
|
0.726
|
0.42
|
1.10
|
0
|
1.001
|
|
lambda[3]
|
NA
|
10000
|
0.399
|
0.324
|
0.14
|
0.63
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8344
|
0.366
|
0.335
|
0.15
|
0.55
|
0
|
1.001
|
|
lambda[5]
|
NA
|
7705
|
0.961
|
0.857
|
0.55
|
1.35
|
0
|
1.001
|
|
N[64]
|
NA
|
10000
|
0.034
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[27]
|
NA
|
9541
|
2.016
|
2.002
|
1.00
|
3.00
|
0
|
1.0006
|
|
N[75]
|
NA
|
10000
|
0.064
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[30]
|
NA
|
9529
|
1.903
|
2.002
|
1.00
|
3.00
|
0
|
1.0005
|
|
N[101]
|
NA
|
9535
|
0.016
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[64]

N[27]

N[75]

N[30]

N[101]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
lure
|
9307
|
-0.119
|
-0.106
|
-0.31
|
0.05
|
0.60432
|
0.856
|
|
alpha0
|
NA
|
4900
|
-2.643
|
-2.64
|
-2.88
|
-2.39
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9201
|
0.575
|
0.496
|
0.24
|
0.88
|
0
|
1.001
|
|
lambda[2]
|
NA
|
7998
|
0.746
|
0.693
|
0.41
|
1.05
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9341
|
0.388
|
0.333
|
0.14
|
0.62
|
0
|
1.001
|
|
lambda[4]
|
NA
|
8568
|
0.368
|
0.325
|
0.16
|
0.56
|
0
|
1.001
|
|
lambda[5]
|
NA
|
7748
|
0.960
|
0.895
|
0.54
|
1.36
|
0
|
1.001
|
|
N[9]
|
NA
|
9611
|
1.133
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[105]
|
NA
|
8904
|
2.031
|
err
|
1.00
|
3.00
|
err
|
err
|
|
N[115]
|
NA
|
9512
|
0.089
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[83]
|
NA
|
10000
|
0.094
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[42]
|
NA
|
10000
|
0.271
|
err
|
0.00
|
1.00
|
err
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[9]

N[105]

N[115]

N[83]

N[42]

alpha relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
5624
|
-0.298
|
-0.287
|
-0.50
|
-0.09
|
0.06692
|
0.9917
|
|
alpha[2]
|
julianDt
|
6353
|
0.334
|
0.332
|
0.14
|
0.51
|
0.01151
|
0.9997
|
|
alpha0
|
NA
|
3381
|
-2.782
|
-2.758
|
-3.06
|
-2.51
|
0
|
1.001
|
|
lambda[1]
|
NA
|
9381
|
0.529
|
0.451
|
0.23
|
0.82
|
0
|
1.001
|
|
lambda[2]
|
NA
|
7768
|
0.750
|
0.712
|
0.42
|
1.08
|
0
|
1.001
|
|
lambda[3]
|
NA
|
9556
|
0.410
|
0.362
|
0.15
|
0.65
|
0
|
1.001
|
|
lambda[4]
|
NA
|
7727
|
0.382
|
0.32
|
0.16
|
0.58
|
0
|
1.001
|
|
lambda[5]
|
NA
|
4577
|
1.228
|
1.118
|
0.68
|
1.78
|
0
|
1.001
|
|
N[58]
|
NA
|
9630
|
0.040
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[93]
|
NA
|
10000
|
0.064
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[71]
|
NA
|
9154
|
0.019
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[101]
|
NA
|
9680
|
0.026
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[99]
|
NA
|
10000
|
0.034
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[58]

N[93]

N[71]

N[101]

N[99]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
julianDt
|
2780
|
-0.568
|
-0.553
|
-0.84
|
-0.31
|
0.00519
|
1.0001
|
|
alpha[2]
|
julianDtSq
|
2761
|
0.891
|
0.912
|
0.63
|
1.15
|
0
|
1.001
|
|
alpha0
|
NA
|
4654
|
-2.746
|
-2.737
|
-3.00
|
-2.49
|
0
|
1.001
|
|
lambda[1]
|
NA
|
7317
|
0.701
|
0.577
|
0.29
|
1.06
|
0
|
1.001
|
|
lambda[2]
|
NA
|
8674
|
0.644
|
0.624
|
0.36
|
0.93
|
0
|
1.001
|
|
lambda[3]
|
NA
|
8596
|
0.422
|
0.35
|
0.15
|
0.67
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9160
|
0.331
|
0.285
|
0.15
|
0.51
|
0
|
1.001
|
|
lambda[5]
|
NA
|
7130
|
0.988
|
0.923
|
0.56
|
1.38
|
0
|
1.001
|
|
N[41]
|
NA
|
10000
|
0.055
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[42]
|
NA
|
10000
|
0.255
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[4]
|
NA
|
9608
|
0.260
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[37]
|
NA
|
10000
|
1.140
|
err
|
1.00
|
2.00
|
err
|
err
|
|
N[49]
|
NA
|
9635
|
0.040
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[41]

N[42]

N[4]

N[37]

N[49]

julian date relationship

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha[1]
|
lureDays
|
5327
|
-0.211
|
-0.208
|
-0.41
|
-0.01
|
0.26016
|
0.9544
|
|
alpha[2]
|
julianDt
|
2609
|
-0.431
|
-0.454
|
-0.72
|
-0.14
|
0.06676
|
0.991
|
|
alpha[3]
|
julianDtSq
|
2765
|
0.854
|
0.835
|
0.60
|
1.12
|
0
|
1.001
|
|
alpha0
|
NA
|
3934
|
-2.819
|
-2.823
|
-3.08
|
-2.54
|
0
|
1.001
|
|
lambda[1]
|
NA
|
7882
|
0.635
|
0.545
|
0.27
|
0.97
|
0
|
1.001
|
|
lambda[2]
|
NA
|
8333
|
0.631
|
0.582
|
0.34
|
0.90
|
0
|
1.001
|
|
lambda[3]
|
NA
|
8832
|
0.423
|
0.351
|
0.15
|
0.67
|
0
|
1.001
|
|
lambda[4]
|
NA
|
9285
|
0.340
|
0.292
|
0.14
|
0.51
|
0
|
1.001
|
|
lambda[5]
|
NA
|
5369
|
1.158
|
1.056
|
0.64
|
1.67
|
0
|
1.001
|
|
N[112]
|
NA
|
8911
|
0.214
|
err
|
0.00
|
1.00
|
err
|
err
|
|
N[79]
|
NA
|
10000
|
1.078
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[87]
|
NA
|
10000
|
1.676
|
1
|
1.00
|
2.00
|
0
|
1.0004
|
|
N[50]
|
NA
|
9679
|
0.038
|
err
|
0.00
|
0.00
|
err
|
err
|
|
N[55]
|
NA
|
10000
|
0.053
|
err
|
0.00
|
0.00
|
err
|
err
|
alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[112]

N[79]

N[87]

N[50]

N[55]

summary table
|
param
|
covariate
|
iters_ef
|
mean
|
mode
|
hdi_89pct_lower
|
hdi_89pct_upper
|
bayes_P
|
pct.density
|
|
alpha
|
counts
|
8949
|
6.936
|
6.22
|
4.88
|
8.89
|
0
|
1.001
|
|
alpha0
|
NA
|
10220
|
-7.500
|
-7.058
|
-9.12
|
-5.89
|
0
|
1.001
|
|
lambda[1]
|
NA
|
10000
|
0.986
|
0.861
|
0.44
|
1.50
|
0
|
1.001
|
|
lambda[2]
|
NA
|
9384
|
0.983
|
0.907
|
0.55
|
1.40
|
0
|
1.001
|
|
lambda[3]
|
NA
|
8756
|
0.970
|
0.792
|
0.34
|
1.53
|
0
|
1.0009
|
|
lambda[4]
|
NA
|
6875
|
0.961
|
0.853
|
0.39
|
1.50
|
0
|
1.001
|
|
lambda[5]
|
NA
|
10000
|
0.986
|
0.932
|
0.57
|
1.38
|
0
|
1.001
|
|
N[103]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[76]
|
NA
|
9245
|
0.939
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[27]
|
NA
|
0
|
1.000
|
err
|
1.00
|
1.00
|
err
|
err
|
|
N[96]
|
NA
|
9341
|
0.940
|
0
|
0.00
|
2.00
|
1
|
err
|
|
N[58]
|
NA
|
9344
|
0.950
|
0
|
0.00
|
2.00
|
1
|
err
|
alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[103]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[76]

N[27]
## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[96]

N[58]

alpha relationship
